I am performing some Molecular Dynamics computer simulations and I am learning about the various Force Fields (FF) such as OPLS-AA, OPLS-UA, AMBER, etc. Many things are still unclear to me. I put these questions together because I think they are strictly related.
1) What is exactly the difference between "Force Field" and "topology", since they define similar parameters?
2) Which parameters can be defined as "belonging" to the FF, and which not? It seems to me that sometimes topology files recall atoms from the force field and edit some parameters such as charge, mass, bond lengths, elastic constants.
3) Why is water model usually considered separately from the FF, and why is it not included in it?
4) When a molecule does not belong to a known topology and we have to model it, how do we establish the compatibility between our model and the FF used for the other molecules in the same simulation?